Health and Genetic Ancestry Testing: Time to Bridge the Gap Andrew Smart1* , Deborah A
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Analysis of Y-Chromosome Polymorphisms in Pakistani
ANALYSIS OF Y-CHROMOSOME POLYMORPHISMS IN PAKISTANI POPULATIONS Thesis submitted to the Sindh Institute of Medical Sciences for the degree of Doctor of Philosophy. BY Sadaf Firasat Centre of Human Genetics and Molecular Medicine Sindh Institute of Medical Sciences Sindh Institute of Urology and Transplantation (SIUT) Karachi, Pakistan 2010 TABLE OF CONTENTS Title page Acknowledgements ii List of Tables iii List of Figures iv Summary vi Introduction 1 Literature Review 19 Materials and Methods 34 Results Phylogeography of Pakistani ethnic groups. 51 Comparison between the Pakistani and Greek populations 73 Discussion 86 Comparison within Pakistan 88 Comparison between the Pakistani and Greek population 94 Comparison with world populations 98 Insight in to populations origins 111 Conclusions 121 References 122 Appendix a i ACKNOWLEDGEMENT I thank Prof. Dr. Syed Qasim Mehdi H.I. S.I., for his support, encouragement and for providing all the facilities for doing scientific work in his laboratory. The work presented in this thesis was done under the supervision of Dr. Qasim Ayub T.I. It is great pleasure for me to acknowledge the keen interest, advice, patient guidance and kindness that I have received from him during the course of this work. I would like to thank Dr. Shagufta Khaliq, (PoP), for teaching all the molecular genetics lab techniques and also to Dr Aiysha Abid for comments on this manuscript and suggestion for its improvement. I am also grateful to Mrs. Ambreen Ayub for her help in making the contour map. I thank my colleague Ms. Sadia Ajaz for her help and cooperation in proof reading the thesis. -
Analysis of Complete Mitochondrial Genomes of Patients with Schizophrenia and Bipolar Disorder
Journal of Human Genetics (2011) 56, 869–872 & 2011 The Japan Society of Human Genetics All rights reserved 1434-5161/11 $32.00 www.nature.com/jhg SHORT COMMUNICATION Analysis of complete mitochondrial genomes of patients with schizophrenia and bipolar disorder Cinzia Bertolin1,4, Chiara Magri2,4, Sergio Barlati2, Andrea Vettori1, Giulia Ida Perini3, Pio Peruzzi3, Maria Luisa Mostacciuolo1 and Giovanni Vazza1 The present study aims at investigating the association between common and rare variants of mitochondrial DNA (mtDNA), and increased risk of schizophrenia (SZ) and bipolar disorder (BPD) in a cohort of patients originating from the same Italian population. The distribution of the major European mtDNA haplogroups was determined in 89 patients and their frequencies did not significantly differ from those observed in the Italian population. Moreover, 27 patients with high probability of having inherited the disease from the maternal side were selected for whole mitochondrial genome sequencing to investigate the possible presence of causative point mutations. Overall, 213 known variants and 2 novel changes were identified, but none of them was predicted to have functional effects. Hence, none of the sequence changes we found in our sample could explain the maternal component of SZ and BPD predisposition. Journal of Human Genetics (2011) 56, 869–872; doi:10.1038/jhg.2011.111; published online 13 October 2011 Keywords: bipolar disorder; mtDNA variants; schizophrenia INTRODUCTION segregation of SZ or BPD, as well as the co-segregation of both phenotypes, have Schizophrenia (SZ) and bipolar disorder (BPD) are among the top ten been observed. This is in agreement with the hypothesis of a genetic overlap causes of disability worldwide.1 Despite extensive genetic and phar- between SZ and BPD; in this study, we hence considered both SZ and BPD cases. -
Supplementary Figures
Supplementary Figures Supplementary Figure S1. Frequency distribution maps for mtDNA haplogroups K, U8a1a and U8b1. Maps created using Surfer and based on the data presented in Supplementary Table S2. Dots represent sampling locations used for the spatial analysis. 1 Supplementary Figure S2. Distribution map of the diversity measure ρ for haplogroup K. Map created using Surfer. Dots represent sampling locations used for the spatial analysis. 2 Supplementary Figure S3. Bayesian skyline plots based on haplogroup U8 mitogenome data in the Near East/Caucasus and Europe. The hypothetical effective population size is indicated (on a logarithmic scale) through time (ka). The sample sizes were 106 and 474 respectively. The posterior effective population size through time is represented by the black line. The blue region represents the 95% confidence interval. 3 Supplementary Figure S4. Reduced-median network of haplogroup K1a9, in the context of putative clade K1a9’10’15’26’30. The network is rooted with several additional lineages from K1a. The tree in Supplementary Data 1 is resolved by assuming transitions first at position 16093 and then at position 195, with K1a20, K1a28 and K1a30 branching off earlier. The tree could also be resolved by assuming mutation at position 195 first, then at 16093, in which case K1a13, K1a16 and K1a31 would branch off earlier, rather than forming a distinct terminal subclade, K1a13’16’31. The latter resolution would considerably extend the European ancestry of the K1a9 lineage. 4 Supplementary Figure S5. Phylogenetic tree of Ashkenazi founders within haplogroup H5. Time scale (ka) based on ML estimations for mitogenome sequences. 5 Supplementary Figure S6. -
A War-Prone Tribe Migrated out of Africa to Populate the World
A war-prone tribe migrated out of Africa to populate the world. Eduardo Moreno1. 1 CNIO, Melchor Fernández Almagro, 3. Madrid 28029, Spain. Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder1,2,3,4,5. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve conflicts. This, in the light of the “recent out of Africa” hypothesis”6,7, suggests that the tribe that left Africa 80.000 years ago performed ritualized fights. In contrast to the more pacific tradition of non-L3 foragers, it may also have had a tendency towards combat. The data implicate that the entire human population outside Africa is descended from only two closely related sub-branches of L3 that practiced ritual fighting and probably had a higher propensity towards warfare and the use of murder for conflict resolution. This may have crucially influenced the subsequent history of the world. There is little evidence for the practice of war before the late Paleolithic3,4. -
Maximizing Mtdna Testing Potential with the Generation of High-Quality Mtgenome Reference Data Author(S): Rebecca S
The author(s) shown below used Federal funding provided by the U.S. Department of Justice to prepare the following resource: Document Title: Maximizing mtDNA Testing Potential with the Generation of High-Quality mtGenome Reference Data Author(s): Rebecca S. Just, Walther Parson, Jodi A. Irwin Document Number: 253077 Date Received: July 2019 Award Number: 2011-MU-MU-K402 This resource has not been published by the U.S. Department of Justice. This resource is being made publically available through the Office of Justice Programs’ National Criminal Justice Reference Service. Opinions or points of view expressed are those of the author(s) and do not necessarily reflect the official position or policies of the U.S. Department of Justice. Final Technical Report to the National Institute of Justice on Award Number 2011-MU-MU-K402 Maximizing mtDNA Testing Potential with the Generation of High-Quality mtGenome Reference Data Authors: a,b c,d a,b,e Rebecca S. Just , Walther Parson and Jodi A. Irwin aArmed Forces DNA Identification Laboratory, 115 Purple Heart Dr., Dover AFB, DE, 19902 bAmerican Registry of Pathology, 9210 Corporate Blvd., Suite 120, Rockville, MD, 20850 cInstitute of Legal Medicine, Innsbruck Medical University, Mllerstrasse 44, Innsbruck, Austria dPenn State Eberly College of Science, 517 Thomas Building, University Park, PA, 16802 eFederal Bureau of Investigation, 2501 Investigation Parkway, Quantico, VA 22135 Recipient Organization: American Registry of Pathology 9210 Corporate Blvd., Suite 120 Rockville, MD 20850 Project Period: April 1, 2011 - March 31, 2015 This resource was prepared by the author(s) using Federal funds provided by the U.S. -
Africa from MIS 6–2: Population Dynamics and Paleoenvironments Sacha C
Africa from MIS 6–2: Population Dynamics and Paleoenvironments Sacha C. Jones and Brian A. Stewart (eds.) Vertebrate Paleobiology and Paleoanthropology Series, Dordrecht: Springer, 2016, 424 pp. (hardback), £103.99. ISBN-13: 9789401775205. Reviewed by DEBORAH I. OLSZEWSKI Department of Anthropology, Penn Museum, 3260 South Street, University of Pennsylvania, Philadelphia, PA 19104, USA; [email protected] his volume includes papers from a conference held at ests, they ask if such contexts were biogeographical corri- Tthe McDonald Institute for Archaeological Research in dors or instead might have operated as barriers to move- 2010. The aim of the conference was to examine the his- ment. In particular, rainforests were patchy spots across tories of populations on the African continent through the the landscape during arid periods, and likely not refugia, use of a variety of data sets—archaeology, genetics, pa- partly due to significant deficiencies in food resources for leoenvironments, and paleontology—to reach a more nu- hominins. anced understanding of hominin skeletal and behavioral Part I: The first three chapters in Part I (Coasts) are evolution, how populations were spatially distributed studies from the coastlines of southern Africa. Chapter 2, across Africa, and the impact of climatic factors on group by A.S. Carr, B.M. Chase, and A. Mackay, focuses on the size and movement. The conference participants sought to Middle Stone Age (MSA) in the southern part of South position data from Africa to aid in the construction of theo- Africa. It is an overview of the archaeology in the period retical frameworks and to benefit from frameworks devel- from 170–55 kya, which is derived primarily from cave and oped elsewhere. -
Whole Mitochondrial Genome Sequencing Highlights Mitochondrial Impact in Gastric Cancer Giovanna Chaves Cavalcante1,2, Anderson N
www.nature.com/scientificreports OPEN Whole mitochondrial genome sequencing highlights mitochondrial impact in gastric cancer Giovanna Chaves Cavalcante1,2, Anderson N. R. Marinho1, Ana Karyssa Anaissi2, Tatiana Vinasco-Sandoval 1, André Ribeiro-dos-Santos1,2, Amanda Ferreira Vidal1, Gilderlanio S. de Araújo1, Samia Demachki2 & Ândrea Ribeiro-dos-Santos 1,2* Mitochondria are organelles that perform major roles in cellular operation. Thus, alterations in mitochondrial genome (mtGenome) may lead to mitochondrial dysfunction and cellular deregulation, infuencing carcinogenesis. Gastric cancer (GC) is one of the most incident and mortal types of cancer in Brazil, particularly in the Amazon region. Here, we sequenced and compared the whole mtGenome extracted from FFPE tissue samples of GC patients (tumor and internal control – IC) and cancer-free individuals (external control – EC) from this region. We found 3-fold more variants and up to 9-fold more heteroplasmic regions in tumor when compared to paired IC samples. Moreover, tumor presented more heteroplasmic variants when compared to EC, while IC and EC showed no signifcant diference when compared to each other. Tumor also presented substantially more variants in the following regions: MT-RNR1, MT-ND5, MT-ND4, MT-ND2, MT-DLOOP1 and MT-CO1. In addition, our haplogroup results indicate an association of Native American ancestry (particularly haplogroup C) to gastric cancer development. To the best of our knowledge, this is the frst study to sequence the whole mtGenome from FFPE samples and to apply mtGenome analysis in association to GC in Brazil. Mitochondria are cytoplasmic organelles that perform major roles in cell operation, including energy generation through oxidative phosphorylation (OXPHOS), cell death, calcium levels control, lipid homeostasis and meta- bolic cell signaling1. -
A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations Spring 2011 A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography Matthew Dulik University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Archaeological Anthropology Commons, Biological and Physical Anthropology Commons, Genetics Commons, and the Molecular Genetics Commons Recommended Citation Dulik, Matthew, "A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography" (2011). Publicly Accessible Penn Dissertations. 1545. https://repository.upenn.edu/edissertations/1545 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1545 For more information, please contact [email protected]. A Molecular Anthropological Study of Altaian Histories Utilizing Population Genetics and Phylogeography Abstract This dissertation explores the genetic histories of several populations living in the Altai Republic of Russia. It employs an approach combining methods from population genetics and phylogeography to characterize genetic diversity in these populations, and places the results in a molecular anthropological context. Previously, researchers used anthropological, historical, ethnographic and linguistic evidence to categorize the indigenous inhabitants of the Altai into two groups – northern and southern Altaians. Genetic data obtained in this study were -
Reduced-Median-Network Analysis of Complete Mitochondrial DNA
Am. J. Hum. Genet. 70:1152–1171, 2002 Reduced-Median-Network Analysis of Complete Mitochondrial DNA Coding-Region Sequences for the Major African, Asian, and European Haplogroups Corinna Herrnstadt,1 Joanna L. Elson,3 Eoin Fahy,1 Gwen Preston,1 Douglass M. Turnbull,3 Christen Anderson,1 Soumitra S. Ghosh,1 Jerrold M. Olefsky,2 M. Flint Beal,4,* Robert E. Davis,1,† and Neil Howell1,5 1MitoKor and 2Veterans Administration Medical Center, San Diego; 3Department of Neurology, University of Newcastle upon Tyne, Newcastle upon Tyne; 4Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and 5Department of Radiation Oncology, University of Texas Medical Branch, Galveston The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small number of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups. Approximately one-half of these polymorphisms are reported for the first time here. Our results confirm and substantially extend the phylogenetic relationships among mitochondrial genomes described elsewhere from the major human ethnic groups. -
Mitochondrial Genomes Uncover the Maternal History of the Pamir Populations
European Journal of Human Genetics (2018) 26:124–136 https://doi.org/10.1038/s41431-017-0028-8 ARTICLE Mitochondrial genomes uncover the maternal history of the Pamir populations 1 2,3 1,4 1 5 6 Min-Sheng Peng ● Weifang Xu ● Jiao-Jiao Song ● Xing Chen ● Xierzhatijiang Sulaiman ● Liuhong Cai ● 1 1 1 7 7 He-Qun Liu ● Shi-Fang Wu ● Yun Gao ● Najmudinov Tojiddin Abdulloevich ● Manilova Elena Afanasevna ● 7 8,9 8,9 8,9 10 Khudoidodov Behruz Ibrohimovich ● Xi Chen ● Wei-Kang Yang ● Miao Wu ● Gui-Mei Li ● 11 12,13 12,14,15 2 1,11,14,15 Xing-Yan Yang ● Allah Rakha ● Yong-Gang Yao ● Halmurat Upur ● Ya-Ping Zhang Received: 15 April 2017 / Revised: 8 September 2017 / Accepted: 6 October 2017 / Published online: 29 November 2017 © European Society of Human Genetics 2018 Abstract The Pamirs, among the world’s highest mountains in Central Asia, are one of homelands with the most extreme high altitude for several ethnic groups. The settlement history of modern humans on the Pamirs remains still opaque. Herein, we have sequenced the mitochondrial DNA (mtDNA) genomes of 382 individuals belonging to eight populations from the Pamirs and the surrounding lowlands in Central Asia. We construct the Central Asian (including both highlanders and lowlanders) fi 1234567890 mtDNA haplogroup tree at the highest resolution. All the matrilineal components are assigned into the de ned mtDNA haplogroups in East and West Eurasians. No basal lineages that directly emanate from the Eurasian founder macrohaplogroups M, N, and R are found. Our data support the origin of Central Asian being the result of East–West Eurasian admixture. -
Exploratory Analysis of Mtdna Haplogroups in Two Alzheimer's
Received: 24 January 2020 Revised: 6 April 2020 Accepted: 29 April 2020 DOI: 10.1002/alz.12119 FEATURED ARTICLE Exploratory analysis of mtDNA haplogroups in two Alzheimer’s longitudinal cohorts Russell H. Swerdlow1 Dongwei Hui1 Prabhakar Chalise1 Palash Sharma1 Xinkun Wang2 Shea J. Andrews3 Judy Pa4 Jonathan D. Mahnken1 Jill Morris1 Heather M. Wilkins1 Jeffrey M. Burns1 Mary L. Michaelis1 Elias K. Michaelis1 For the Alzheimer’s Disease Neuroimaging Initiative (ADNI)∗ 1 Alzheimer’s Disease Center, University of Kansas Medical Center, Kansas City, Kansas, Abstract USA Introduction: Inherited mitochondrial DNA (mtDNA) variants may influence 2 Feinberg School of Medicine, Northwestern Alzheimer’s disease (AD) risk. University, Chicago, Illinois, USA 3 Ronald M. Loeb Center for Alzheimer’s Methods: We sequenced mtDNA from 146 AD and 265 cognitively normal (CN) sub- Disease, Icahn School of Medicine at Mount jects from the University of Kansas AD Center (KUADC) and assigned haplogroups. We Sinai, New York, New York, USA further considered 244 AD and 242 CN AD Neuroimaging Initiative (ADNI) subjects 4 Alzheimer’s Disease Research Center, Mark and Mary Stevens Neuroimaging and with equivalent data. Informatics InstituteUniversity of Southern Results: Without applying multiple comparisons corrections, KUADC haplogroup J AD California, Los Angeles, California, USA and CN frequencies were 16.4% versus 7.6% (P = .007), and haplogroup K AD and CN Correspondence frequencies were 4.8% versus 10.2% (P = .063). ADNI haplogroup J AD and CN fre- Russell H. Swerdlow, MD, University of Kansas quencies were 10.7% versus 7.0% (P = .20), and haplogroup K frequencies were 4.9% Alzheimer’s Disease Center, 4350 Shawnee Mission Parkway, Fairway, KS 66205, USA. -
Mtdna Variation in the South African Kung and Khwe—And Their Genetic Relationships to Other African Populations Yu-Sheng Chen,1,* Antonel Olckers,4 Theodore G
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Am. J. Hum. Genet. 66:1362–1383, 2000 mtDNA Variation in the South African Kung and Khwe—and Their Genetic Relationships to Other African Populations Yu-Sheng Chen,1,* Antonel Olckers,4 Theodore G. Schurr,1,2,† Andreas M. Kogelnik,1,3 Kirsi Huoponen,1,‡ and Douglas C. Wallace1,2 1Center for Molecular Medicine and 2Department of Anthropology, Emory University, and 3Program in Biomedical Engineering, College of Computing, Georgia Institute of Technology, Atlanta; and 4Department of Human Genetics, University of Pretoria, Pretoria The mtDNA variation of 74 Khoisan-speaking individuals (Kung and Khwe) from Schmidtsdrift, in the Northern Cape Province of South Africa, was examined by high-resolution RFLP analysis and control region (CR) sequencing. The resulting data were combined with published RFLP haplotype and CR sequence data from sub-Saharan African populations and then were subjected to phylogenetic analysis to deduce the evolutionary relationships among them. More than 77% of the Kung and Khwe mtDNA samples were found to belong to the major mtDNA lineage, macrohaplogroup L* (defined by a HpaI site at nucleotide position 3592), which is prevalent in sub-Saharan African populations. Additional sets of RFLPs subdivided macrohaplogroup L* into two extended haplogroups—L1 and L2—both of which appeared in the Kung and Khwe. Besides revealing the significant substructure of macrohap- logroup L* in African populations, these data showed that the Biaka Pygmies have one of the most ancient RFLP sublineages observed in African mtDNA and, thus, that they could represent one of the oldest human populations.